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Magnesium in PDB 4ied: Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum

Enzymatic activity of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum

All present enzymatic activity of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum, PDB code: 4ied was solved by S.Mangani, M.Benvenuti, J.D.Docquier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.59 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.945, 65.670, 91.698, 84.59, 82.91, 70.12
R / Rfree (%) 14.6 / 18.4

Other elements in 4ied:

The structure of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum (pdb code 4ied). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum, PDB code: 4ied:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 4ied

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Magnesium binding site 1 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:19.5
occ:1.00
 O A:HOH871 2.0 32.4 1.0
O A:HOH565 2.1 15.0 1.0
O A:HOH623 2.1 20.9 1.0
O A:HOH782 2.1 31.3 1.0
O A:HOH700 2.2 23.5 1.0
O A:HOH800 2.3 25.2 1.0
OE1 A:GLU216 4.1 14.7 1.0
O A:HOH611 4.1 15.3 1.0
O A:HOH667 4.1 24.8 1.0
OE2 A:GLU216 4.2 14.8 1.0
O A:SER165 4.3 7.8 1.0
NZ A:LYS180 4.6 8.2 1.0
CD A:GLU216 4.6 12.6 1.0
CA A:GLN166 4.8 8.7 1.0
O A:HOH810 5.0 28.8 1.0

Magnesium binding site 2 out of 12 in 4ied

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Magnesium binding site 2 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:17.1
occ:1.00
 O A:HOH503 2.0 15.1 1.0
O A:HOH593 2.0 17.6 1.0
O A:HOH582 2.0 21.1 1.0
O A:HOH578 2.2 16.1 1.0
O A:HOH487 2.2 12.0 1.0
O A:HOH613 2.2 19.1 1.0
OE1 A:GLU78 3.7 9.7 1.0
O A:HOH788 4.0 26.7 1.0
O A:HOH519 4.1 15.2 1.0
O A:HOH526 4.1 17.7 1.0
O A:HOH631 4.1 18.3 1.0
O A:MET79 4.2 7.8 1.0
O A:ILE72 4.3 7.8 1.0
CD A:GLU78 4.3 9.7 1.0
O A:HOH806 4.8 32.5 1.0
CD1 A:PHE80 4.8 6.1 1.0
OE2 A:GLU78 4.9 12.3 1.0

Magnesium binding site 3 out of 12 in 4ied

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Magnesium binding site 3 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:7.6
occ:1.00
 O B:ASN134 2.3 6.6 1.0
O B:HOH446 2.4 7.3 1.0
OE2 B:GLU136 2.4 7.5 1.0
CD B:GLU136 3.3 7.3 1.0
C B:ASN134 3.4 6.3 1.0
CG B:GLU136 3.5 6.9 1.0
CB B:ASN134 3.8 6.4 1.0
CA B:ASN134 3.9 6.2 1.0
OE1 B:GLU136 4.4 7.8 1.0
N B:LYS135 4.5 6.0 1.0
CG B:ASN134 4.5 6.2 1.0
N B:GLU136 4.8 6.2 1.0
O B:HOH581 4.8 15.9 1.0
C B:LYS135 4.8 6.3 1.0
CB B:GLU136 4.8 6.6 1.0
CB B:LYS135 4.9 6.5 1.0
CA B:LYS135 5.0 6.1 1.0
OD1 B:ASN134 5.0 5.9 1.0

Magnesium binding site 4 out of 12 in 4ied

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Magnesium binding site 4 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:28.1
occ:1.00
 OD1 B:ASN38 1.9 19.4 1.0
O B:HOH550 2.8 21.2 1.0
O B:HOH522 2.8 15.2 1.0
OD2 B:ASP35 2.9 10.0 1.0
CG B:ASN38 3.0 15.4 1.0
ND2 B:ASN220 3.5 9.5 1.0
ND2 B:ASN38 3.6 16.0 1.0
CG B:ASP35 3.8 9.5 1.0
OD1 B:ASP35 3.9 9.7 1.0
OH B:TYR222 3.9 9.3 1.0
CB B:ASN38 4.2 14.5 1.0
O B:HOH772 4.3 34.0 1.0
CE2 B:TYR222 4.6 8.6 1.0
CZ B:TYR222 4.7 8.6 1.0
O B:HOH506 4.8 12.3 1.0
CG B:ASN220 4.8 9.2 1.0
N B:ASN38 4.9 12.8 1.0

Magnesium binding site 5 out of 12 in 4ied

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Magnesium binding site 5 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:40.1
occ:1.00
 O B:HOH514 2.1 16.3 1.0
O B:HOH527 2.3 27.5 1.0
O B:HOH570 2.4 15.1 1.0
O B:GLU117 3.6 8.3 1.0
CB B:GLU117 3.7 7.9 1.0
CG B:GLU117 4.0 8.3 1.0
CA B:GLU117 4.0 7.9 1.0
C B:GLU117 4.1 7.9 1.0
OE2 B:GLU117 4.1 9.6 1.0
NH2 B:ARG122 4.3 9.1 1.0
CD B:GLU117 4.5 9.0 1.0
O B:HOH648 4.7 24.9 1.0
O B:HOH472 4.9 12.7 1.0
CD1 B:ILE72 4.9 9.0 1.0

Magnesium binding site 6 out of 12 in 4ied

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Magnesium binding site 6 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:13.5
occ:1.00
 O C:ASN134 2.2 8.3 1.0
OE2 C:GLU136 2.4 10.2 1.0
O C:HOH461 2.5 12.0 1.0
C C:ASN134 3.3 7.8 1.0
CD C:GLU136 3.3 10.0 1.0
CG C:GLU136 3.6 9.6 1.0
CB C:ASN134 3.8 8.2 1.0
CA C:ASN134 3.8 7.8 1.0
N C:LYS135 4.4 7.5 1.0
OE1 C:GLU136 4.5 10.7 1.0
CG C:ASN134 4.5 8.2 1.0
C C:LYS135 4.7 7.7 1.0
N C:GLU136 4.7 7.8 1.0
CB C:LYS135 4.7 7.5 1.0
O C:HOH413 4.8 13.6 1.0
CA C:LYS135 4.8 7.5 1.0
CB C:GLU136 4.8 8.8 1.0
O C:HOH683 4.9 22.1 1.0
CE C:LYS135 5.0 7.8 1.0
OD1 C:ASN134 5.0 7.9 1.0

Magnesium binding site 7 out of 12 in 4ied

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Magnesium binding site 7 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:14.2
occ:1.00
 O A:HOH627 2.0 18.9 1.0
O C:HOH792 2.1 15.7 1.0
O C:HOH778 2.1 13.5 1.0
O C:HOH766 2.1 15.6 1.0
O A:HOH798 2.1 16.1 1.0
O C:HOH466 2.1 13.1 1.0
O C:HOH527 4.0 21.1 1.0
OD2 C:ASP42 4.1 11.1 1.0
OE2 A:GLU140 4.1 12.4 1.0
O C:HOH522 4.1 17.2 1.0
OD1 C:ASP42 4.2 10.1 1.0
O C:HOH509 4.3 14.8 1.0
O A:HOH559 4.3 17.5 1.0
NZ C:LYS40 4.3 13.4 1.0
CG C:ASP42 4.5 10.0 1.0
OH C:TYR246 4.5 9.7 1.0
O C:HOH650 4.5 25.8 1.0
O A:HOH731 4.6 24.2 1.0
O C:HOH438 4.6 8.2 1.0
CG2 C:ILE250 4.7 17.9 1.0
ND2 C:ASN15 4.8 10.8 1.0
O C:HOH780 5.0 25.3 1.0
O A:HOH648 5.0 25.9 1.0

Magnesium binding site 8 out of 12 in 4ied

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Magnesium binding site 8 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.7
occ:1.00
 O C:HOH795 2.1 22.7 1.0
O C:HOH465 2.7 13.3 1.0
O C:HOH783 3.4 43.7 1.0
O C:HOH417 3.4 9.7 1.0
O C:HOH725 3.5 29.6 1.0
OG C:SER57 3.7 7.9 1.0
CG2 C:VAL108 3.7 11.8 1.0
O C:HOH580 3.9 17.4 1.0
O C:HOH658 4.0 29.1 1.0
O C:HOH664 4.0 20.8 1.0
O C:HOH666 4.1 30.3 1.0
O C:HOH548 4.2 20.9 1.0
OQ2 C:KCX60 4.6 10.1 1.0
CH2 C:TRP93 4.7 8.2 1.0
O C:HOH670 4.7 19.6 1.0
O C:HOH663 4.8 26.1 1.0
CD2 C:LEU146 4.8 16.4 1.0
O C:TRP199 4.9 9.0 1.0

Magnesium binding site 9 out of 12 in 4ied

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Magnesium binding site 9 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:23.1
occ:1.00
 O C:HOH662 2.0 22.2 1.0
O C:HOH667 2.0 25.4 1.0
O C:HOH796 2.0 24.4 1.0
O C:HOH660 2.0 29.1 1.0
O C:HOH493 2.1 16.4 1.0
O C:HOH652 2.2 24.3 1.0
O C:HOH636 4.0 29.1 1.0
OE2 C:GLU216 4.2 14.8 1.0
O C:HOH536 4.2 18.5 1.0
OE1 C:GLU216 4.3 15.2 1.0
O C:SER165 4.4 10.3 1.0
O C:HOH665 4.5 26.7 1.0
NZ C:LYS180 4.7 10.9 1.0
CD C:GLU216 4.7 14.2 1.0
CA C:GLN166 4.9 10.1 1.0
O C:HOH695 4.9 28.6 1.0

Magnesium binding site 10 out of 12 in 4ied

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Magnesium binding site 10 out of 12 in the Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:18.4
occ:1.00
 O D:HOH502 2.7 15.3 1.0
O D:HOH473 4.3 15.6 1.0
O D:HOH749 4.3 23.3 1.0
OE1 D:GLU140 4.7 12.9 1.0

Reference:

S.Mangani, M.Benvenuti, J.D.Docquier. Crystal Structure of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum To Be Published.
Page generated: Mon Dec 14 18:52:47 2020

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